Beauchamp:MRI Data Analysis

Beauchamp Lab Notebook

• Home
• Lab Members
• Lab Alums
• Projects
• Publications
• Lab Notebook
• Subjects

• Software Installation
• Ordering
• MRI Data Analysis
• Electrophysiology
• TMS

1. Internal Wiki (UTHSC-H Only)

MRI

1. Motion and Distortion Correction
2. Autism Data

MEG and MRI

Download and install MNE Go to http://www.nmr.mgh.harvard.edu/martinos/userinfo/data/MNE_register/index.php and register. After registering you will be emailed a login password. The webpage makes it seem that an email is sent immediately, but in my experience it took over an hour. After you receive your password login and download the software, also available is the manual and installation instructions. Following steps C.1 - C.2.3 should do it, unless your computer doesn't already have fink on it, in which case follow the instructions available on the internal wiki to install fink. One step you'll have to change, C.1.2 instructs you to type "tar zxvf <filename>", however they seem to longer be using gzip format files, so instead change that to "tar -xvf <filename>".

Run MNE GUI (mne_analyze)

Save a label file format for label file is like this

 # Label from mne_analyze
 2358
 16 -39.8716 -10.9534 17.9286 0
 62 -40.1451 7.47006 5.60055 0
 etc.

Try to create a similar label file in SUMA

two ways: 1) Manually drawing an ROI (ctrl-d in SUMA)

2) 3dVol2Surf

Both MNE and AFNI analysis will need to use the EXACT SAME surface because otherwise the node numbering will be different and the ROIs will not correspond.

Here is a possible way to do this, according to Ziad Saad:

1) Create an ROI containing all nodes using 3dVol2Surf -oob or -oob OR draw an ROI, use ROI2dataseet to convert to a file with all nodes

2) cat or 1dcat this file with the original surface file (containing the x,y,z co-ordinates of the nodes)

3) Use convertdset to select only those nodes with a value at the nodes